However, there seems to be a flaw in my lower. The raised area below one of the stops for the selector switch appears to have been milled too low and they attempted to clean it up afterwards and it simply looks like crap. I must say that I am a bit disappointed. I'm not that familiar with the AR-15 platform, so my question is do these raised areas serve any purpose and can I file these down so that they are flat with the receiver?

It shouldn't make any difference. It is just to stop the selector safety switch. If you don't want it let me know